Fluorescent high-density labeling of DNA: error-free substitution for a normal nucleotide

Földes-Papp, Zeno; Angerer, Bernhard; Ankenbauer, W.; Rigler, Rudolf

doi:10.1016/s0168-1656(00)00416-8

Cited by 37 publications

(30 citation statements)

References 38 publications

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“…On the technical side, the following factors can affect the amplitudes of auto-and cross-correlation curves, and hence the experimentally determined K D value; the observation volume elements for the spectrally distinct fluorophores have different volumes and can be displaced due to chromatic aberrations and misaligned excitation lasers, cross-talk between the channels, background fluorescence, and resonance energy transfer between the fluorophores (Förster resonance energy transfer (FRET)). These processes have been recognized and meticulously analyzed in several publications, from the first report by Földes-Papp et al (37) to the recent work by Wohland and co-workers (38) and references therein. The main conclusion of these studies is that technical limitations do not contribute significantly (Ͻ25%) (37), except under conditions when FRET between the fluorophores is very strong (33,35,37,38), which seems not to be the case in our studies.…”

Section: ⅐Ps-tx14(a)mentioning

confidence: 99%

“…These processes have been recognized and meticulously analyzed in several publications, from the first report by Földes-Papp et al (37) to the recent work by Wohland and co-workers (38) and references therein. The main conclusion of these studies is that technical limitations do not contribute significantly (Ͻ25%) (37), except under conditions when FRET between the fluorophores is very strong (33,35,37,38), which seems not to be the case in our studies. For the purpose of our studies, it is most important to ascertain that cross-talk between the channels does not yield a false-positive result.…”

Section: ⅐Ps-tx14(a)mentioning

confidence: 99%

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GPR37 Protein Trafficking to the Plasma Membrane Regulated by Prosaposin and GM1 Gangliosides Promotes Cell Viability

Vukojević

Hertz

Stroth

et al. 2014

Journal of Biological Chemistry

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Background: Intracellular GPR37 accumulation is neurotoxic and associated with parkinsonism, whereas plasma membrane association is protective. Results: The endogenous GPR37 ligand prosaposin promotes GPR37 surface density and association with GM1-enriched lipid rafts. Conclusion: GPR37, prosaposin, and GM1 constitute a pathway that improves cell viability through GPR37 trafficking to the plasma membrane. Significance: Targeting this pathway could reduce toxic intracellular GPR37 accumulation observed in parkinsonism.

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Section: ⅐Ps-tx14(a)mentioning

confidence: 99%

Section: ⅐Ps-tx14(a)mentioning

confidence: 99%

GPR37 Protein Trafficking to the Plasma Membrane Regulated by Prosaposin and GM1 Gangliosides Promotes Cell Viability

Vukojević

Hertz

Stroth

et al. 2014

Journal of Biological Chemistry

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“…46 Random incorporation of plural numbers of fluorescent dye molecules into the PCR product during the reaction may provide improved sensitivity compared to the single 5'-end labeling employed here when fast PCR is required. [47][48][49] PCR runs were next performed with a template concentration of 10 ng mL 21 to determine an upper bound on the linear velocity that could be used using micro-CFPCR for the generation of either a 500 or 997 bp fragment. Fig.…”

mentioning

confidence: 99%

Rapid PCR in a continuous flow device

et al. 2004

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Continuous flow polymerase chain reaction (CFPCR) devices are compact reactors suitable for microfabrication and the rapid amplification of target DNAs. For a given reactor design, the amplification time can be reduced simply by increasing the flow velocity through the isothermal zones of the device; for flow velocities near the design value, the PCR cocktail reaches thermal equilibrium at each zone quickly, so that near ideal temperature profiles can be obtained. However, at high flow velocities there are penalties of an increased pressure drop and a reduced residence time in each temperature zone for the DNA/reagent mixture, that potentially affect amplification efficiency. This study was carried out to evaluate the thermal and biochemical effects of high flow velocities in a spiral, 20 cycle CFPCR device. Finite element analysis (FEA) was used to determine the steady-state temperature distribution along the micro-channel and the temperature of the DNA/reagent mixture in each temperature zone as a function of linear velocity. The critical transition was between the denaturation (95 uC) and renaturation (55 uC-68 uC) zones; above 6 mm s 21 the fluid in a passively-cooled channel could not be reduced to the desired temperature and the duration of the temperature transition between zones increased with increased velocity. The amplification performance of the CFPCR as a function of linear velocity was assessed using 500 and 997 base pair (bp) fragments from l-DNA. Amplifications at velocities ranging from 1 mm s 21 to 20 mm s 21 were investigated. The 500 bp fragment could be observed in a total reaction time of 1.7 min (5.2 s cycle 21) and the 997 bp fragment could be detected in 3.2 min (9.7 s cycle 21 ). The longer amplification time required for detection of the 997 bp fragment was due to the device being operated at its enzyme kinetic limit (i.e., Taq polymerase deoxynucleotide incorporation rate).

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“…Single-molecule DNA-sequencing techniques are still in their infancy, but proof-of-concept experiments demonstrate the possibility of an eventual viable method that could potentially sequence up to 2000 bp s -1 (greatly surpassing the fastest sequencing technique today) [158][159][160][161][162]. Several single-molecule sequencing schemes exist.…”

Section: Single-molecule Dna Detection Sorting and Sequencingmentioning

confidence: 99%